While the morphological variation was important in the creation of koi as they are today, the expression of color is certainly central to defining koi as ornamental. It is true to say that without colour koi would never have developed. Skin pigment cells produce the various colors. Erythrophores and xanthophores contain carotenoid pigments and produce various shades of red or yellow. Melanophores are black and contain melanin.

In addition, further hues like green and light blue are formed due to the superposition of pigment cells in the skin.

Figure 1. A single zebrafish melanophore imaged by time-lapse photography during pigment aggregation. Because black pigment cells are connected to the central nervous system they can react to the environment sensed by the fish. Click this image to see how the pigment cells of a tilapia respond to a drop of adrenalin, simulating fight-or-flight response, thus causing stress in the fish which in turn triggers the pigment aggrigation..

Leucophores contain granules of guanine resulting in a white appearance. Iridophores contain iridescent plate-like crystals of guanine resulting in a shining, metallic appearance of the skin also known as hikari. In combination with yellow, the effect can be golden (e.g. Ogon) and with white it could be silver like Purachina. Platelets of guanine form in the scale structure a radiant, reflecting surface known as ginrin in the scale structure. On a red or yellow background there is a golden reflection and when overlaying black, blue or white, silver is reflected. This is where the kinginrin designation comes from: gold-silver-scale.

Figure 2. Iridophores appear as different types of ginrin, eg.A. Beta-gin, also called Niigata ginrin is more lumpy and dull; B. Dia-gin or Hiroshima ginrin has larger crystal platelets reflective in many angles and is very popular. Notice how the colour changes depending on the underlying ground colour.

Cyanophores contain a blue pigment of unknown chemical composition. The melanophores and cyanophores pigments are stored in fibrous organelles that can open or contract under control of the central nervous system. Chromatosomes are derived from the neural crest and migrate to their positions during ontology (development) of the embryo. The melanophores and cyanophores follow the internal route while the other future pigment cells migrate alone to the outer layers of the dermis. This could be the reason why red, yellow and white appeared to be overlaying black and blue initially.

Figure 3. Cross-section scheme of developing vertebrate embryo. Both paths of the neural crest colour cells migration are marked by arrows: red for erythrophores, xanthophores and leucophores along the skin of the embryo, while in blue, melanophores and cyanophores migrating much deeper in the animal. (1 – neural crest, 2 – neural tube, 3 – dorsal somite, 4 – notochord.)

Aspects of chromatophores that are exploited during breeding and selection of koi are: (1) pigment cell formation and migration; (2) pigment synthesis; (3) pigment cell translocation; (4) visual pigment cell interaction between the two main groups of chromatophores (xanthophore-like and melanophore-like cells) and (5) time dependency of all these over the life of the individual.

Melanophores are cells found on the skin and/or scales of many aquatic vertebrates including fish and amphibians. These are large cells which contain many dark pigment particles called melanosomes, made dark by the presence of the pigment melanin. These melanosomes move along microtubular tracks within the cell by motor proteins and can be rearranged to be dispersed within the cell (maximising light absorption by the melanosomes) or condensed near the centrosome (minimising light absorption). Organisms with melanophores trigger this movement of the melanosomes to change colour in response to stimuli.

Chromatophores are pigment-containing and light-reflecting cells, or groups of cells, found in a wide range of animals including amphibians, fish, reptiles, crustaceans and cephalopods.

Neural crest cells are a temporary group of cells unique to vertebrates that arise from the embryonic ectoderm cell layer, and in turn give rise to a diverse cell lineage—including melanocytes, craniofacial cartilage and bone, smooth muscle, peripheral and enteric neurons and glia.

Neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord.

Ectoderm is one of the three primary germ layers in the very early embryo. The other two layers are the mesoderm (middle layer) and endoderm (most proximal layer), with the ectoderm as the most exterior (or distal) layer. It emerges and originates from the outer layer of germ cells.

Somites are bilaterally paired blocks of paraxial mesoderm that form along the head-to-tail axis of the developing embryo in segmented animals.